utils

preproc_huII

pull_seq_huII

prep_lbl_huII

comb_pred_tbl

find_nonself_huII

pull_ag_self

find_core_mut

preproc_huII() format and validate allele names

A suite of tools to predict peptide MHC (major histocompatibility complex) presentation in the context of both human and mouse. Polymorphic peptides between self and foreign proteins are identified. The ability of peptides to bind self MHC is assessed and scored. Based on half maximal inhibitory concentration as queried through the immune epitope database API <http://tools.iedb.org/mhcii/> using user defined methods, the foreign peptides most likely to be presented are output along with their predicted binding strength, amino acid position, the protein from which each peptide was derived, and the presenting allele. "References:" Vita R, Mahajan S, Overton JA, Dhanda SK, Martini S, Cantrell JR, Wheeler DK, Sette A, Peters B. <doi:10.1093/nar/gky1006>.

Joan Zhang

epitopR

Predict Peptide-MHC Binding

Aileen Johnson

Christian P Larsen

utils function

<dl><dt>allele_in</dt>
<dd>a vector contains allele name(s)
pull_seq_huII() pull out sequence of each allele based on ref table</dd>
<dt>alleles_in</dt>
<dd>vector, allele names
comb_pred_tbl() combine individual prediction tables by method, exclude none-binders and keep strong and weak binders only</dd>
<dt>tbl_ref_in</dt>
<dd>dataframe, reference table, default is human_all.csv from github
prep_lbl_huII() concatenate allele strings for prediction table names</dd>
<dt>nm_method</dt>
<dd>string, prediction method used for IEDB prediction</dd>
<dt>nm_sht</dt>
<dd>string, short name of alleles</dd>
<dt>nm_fd</dt>
<dd>string, folder name which contains predict tables from IEDB</dd>
<dt>thold_score</dt>
<dd>list of vectors, binder thresholds by score</dd>
<dt>thold_rank</dt>
<dd>vector, binder thresholds by rank
find_nonself_huII() find nonself binding peptides</dd>
<dt>dat_in</dt>
<dd>dataframe with pep_stim, core, pep_self selected from pull_ag_self</dd></dl>

Arguments

Basic functions of the package — utils

<dl>

<dt>allele_in</dt>
<dd>a vector contains allele name(s)
pull_seq_huII() pull out sequence of each allele based on ref table</dd>


<dt>alleles_in</dt>
<dd>vector, allele names
comb_pred_tbl() combine individual prediction tables by method, exclude none-binders and keep strong and weak binders only</dd>


<dt>tbl_ref_in</dt>
<dd>dataframe, reference table, default is human_all.csv from github
prep_lbl_huII() concatenate allele strings for prediction table names</dd>


<dt>nm_method</dt>
<dd>string, prediction method used for IEDB prediction</dd>


<dt>nm_sht</dt>
<dd>string, short name of alleles</dd>


<dt>nm_fd</dt>
<dd>string, folder name which contains predict tables from IEDB</dd>


<dt>thold_score</dt>
<dd>list of vectors, binder thresholds by score</dd>


<dt>thold_rank</dt>
<dd>vector, binder thresholds by rank
find_nonself_huII() find nonself binding peptides</dd>


<dt>dat_in</dt>
<dd>dataframe with pep_stim, core, pep_self selected from pull_ag_self</dd>

</dl>

Basic functions of the package

utils: Basic functions of the package

Description

Usage

Arguments